Synopsis

Demonstration code for Functional Pearl: Signature Memoization for Drug Repurposing at Declarative Programming in Biology and Medicine (DeclMed) 2023.

Talk recording

Upstream repositories

See also the following upstream repositories:

https://github.com/jeffhhk/dagopoly-py https://github.com/jeffhhk/dagopoly-scm

Instructions

Prerequisites

Tested with software versions:

• Python 3.7.9
• Chez Scheme 9.5

To run the demo application, you will need to obtain a copy of RTX-KG2c version 7.6. The redistribution license terms of RTX-KG2c (in the words of its authors) are It's complicated. Unfortunately, they currently have not posted a new enough version of this particular artifact to be suitabl for the demo. Contact the author to arrange access: jeff at groovescale dot com.

Setup

Clone this repository. Make the local repository your current directory.

Obtain rtx-kg2c_7.6.tar.gz and copy to dagopoly-py/storage/exogenous/

Demonstration 1 - minimal Python application

python dagopoly-py/test/autobin/test1.py

Demonstration 2 - minimal Scheme application

bash dagopoly-scm/chezscheme.sh --script dagopoly-scm/test/adhoc/minimal-program.scm

Demonstration 3 - Scheme to Python IPC

bash dagopoly-scm/chezscheme.sh --script dagopoly-scm/test/adhoc/test-ipc-send.chezscheme.scm

Demonstration 4 - Drug Repurposing candidates for Alzheimer’s Disease

python alz/alz.py

Footnotes

If you are using this repository, scheme dependencies from akku will be checked in.